"""Read Siemens Syngo.VIA Basic Reading
"""
# Copyright (c) 2017-2024 Erling Andersen, Haukeland University Hospital, Bergen, Norway
import numpy as np
import logging
from .ROI import PolygonROI, EllipseROI
logger = logging.getLogger(__name__)
def _xyz_to_zyx(polygon):
"""Swap (x,y,z) with (z,y,x) for each point
Args:
polygon: np.array shape (n,3)
Returns:
rearranged np.array shape (n,3)
"""
assert polygon.ndim == 2, "Array ndim should be 2, not {}".format(polygon.ndim)
new_polygon = np.zeros_like(polygon)
for i in range(polygon.shape[0]):
x, y, z = polygon[i, :]
new_polygon[i, :] = z, y, x
return new_polygon
def _get_measurement_points(output, point=True, zyx=False):
if output.VR == "UN":
meas_data_points = np.fromstring(output.value, dtype='float32')
else:
meas_data_points = np.array(output.value)
if point:
points = meas_data_points.reshape((meas_data_points.size // 3, 3))
else:
points = meas_data_points
if point and zyx:
logger.debug("XYZ: {}".format(points[0]))
points = _xyz_to_zyx(points)
logger.debug("ZYX: {}".format(points[0]))
return points
[docs]
def evidence2roi(im, uid_table=None, content=None):
# def get_rois(image, separate_laterality=False, uid_table=None, content={}):
"""
overrows = image[(0x6000, 0x0010)].value
overcols = image[(0x6000, 0x0011)].value
overkey=(0x6000, 0x3000)
overlay=image[overkey].value
a=bitarray.bitarray(overlay, endian='little')
while len(a) < len(overlay)*8:
a.append(0)
c = np.array(a.tolist())
c = c.astype(np.uint8)
#c = c.reshape((overcols, overrows))
c = c.reshape((overrows, overcols))
"""
# print("get_rois: {}".format(image.InstanceNumber))
# content = {}
if content is None:
content = {}
rois = [] # List of ROI tuples
seqkey = (0x0029, 0x1102)
if seqkey in im:
presentation_sq = im[seqkey]
else:
seqkey = (0x0029, 0x1202)
if seqkey not in im:
logger.debug("get_rois: no presentation sequence (0x0029, 0x1202)")
return rois, content
presentation_sq = im[seqkey]
try:
measurements = presentation_sq[0][(0x0029, 0x10a7)]
except (TypeError, KeyError):
try:
p0_sq = presentation_sq[0][(0x0029, 0x10ee)]
measurements = p0_sq[0][(0x0029, 0x10a7)]
except (TypeError, KeyError):
logger.debug("get_rois: no measurement sequence (0x0029, 0x10a7)")
raise KeyError('No measurement sequence (0x0029, 0x10a7) in input data')
findings = None
for measurement in measurements:
if (0x0029, 0x1031) in measurement:
findings = measurement[(0x0029, 0x1031)]
if findings is None:
logger.error('get_rois: no findings attribute (0x0029, 0x1031) in input data')
raise KeyError('No findings attribute (0x0029, 0x1031) in input data')
content_sq = presentation_sq[0][(0x0029, 0x10a9)]
content['label'] = content_sq[0][(0x0070, 0x0080)].value
content['description'] = content_sq[0][(0x0070, 0x0081)].value
content['date'] = content_sq[0][(0x0070, 0x0082)].value
content['time'] = content_sq[0][(0x0070, 0x0083)].value
content['creator'] = '%s' % presentation_sq[0][(0x0070, 0x0084)].value
for finding in findings:
referenced_frame_seq = finding[(0x0029, 0x109a)][0]
if referenced_frame_seq[(0x0029, 0x1038)].VM > 1:
referenced_syngo_uid = []
for u in referenced_frame_seq[(0x0029, 0x1038)].value:
referenced_syngo_uid.append(u)
referenced_syngo_uid = referenced_frame_seq[(0x0029, 0x1038)].value
else:
referenced_syngo_uid =\
referenced_frame_seq[(0x0029, 0x1038)].value.decode().split('\\')
if uid_table is not None:
stu_ins_uid = uid_table[referenced_syngo_uid[0]]
ser_ins_uid = uid_table[referenced_syngo_uid[1]]
sop_ins_uid = uid_table[referenced_syngo_uid[2]]
else:
stu_ins_uid = referenced_syngo_uid[0]
ser_ins_uid = referenced_syngo_uid[1]
sop_ins_uid = referenced_syngo_uid[2]
# sop_cla_uid = referenced_syngo_uid[3] # '1.2.840.10008.5.1.4.1.1.4'
# ROI number
meas_appl_number = int(finding[(0x0029, 0x1035)].value)
roi_type_value = finding[(0x0029, 0x1032)].value.strip()
try:
roi_type_value = roi_type_value.decode('ascii')
except AttributeError:
pass
try:
roi_name = finding[(0x0029, 0x1030)].value.decode()
except AttributeError:
roi_name = finding[(0x0029, 0x1030)].value
except KeyError:
roi_name = 'NONAME'
logger.info("Finding: {} {} {}".format(content['creator'], roi_name, roi_type_value))
if roi_type_value == 'PolygonApplication3D' or roi_type_value == 'FreehandApplication3D':
polygon = _get_measurement_points(finding[(0x0029, 0x1096)], zyx=True)
rois.append(PolygonROI(polygon, roi_name, stu_ins_uid, ser_ins_uid, sop_ins_uid))
logger.debug('ROI {}: {} points'.format(meas_appl_number, len(polygon) // 3))
elif roi_type_value == 'MarkerApplication3D':
# marker = _get_measurement_points(finding[(0x0029, 0x1096)], zyx=True)
logger.warning("MarkerApplication3D ROI not implemented.")
elif roi_type_value == 'EllipseApplication3D':
# Ellipsis centre
centre = _get_measurement_points(finding[(0x0029, 0x1096)], zyx=True)
# Ellipsis angles
angles = _get_measurement_points(finding[(0x0029, 0x1097)])
# Ellipsis thickness
thickness = _get_measurement_points(finding[(0x0029, 0x1099)], point=False)
rois.append(EllipseROI(
centre, angles, thickness, roi_name, stu_ins_uid, ser_ins_uid, sop_ins_uid))
elif roi_type_value == 'StandaloneTextApplication3D':
logger.warning("Standalone Text ROI not implemented.")
pass
elif roi_type_value == 'DistanceLineApplication3D':
logger.warning("DistanceLineApplication3D ROI not implemented.")
pass
else:
raise ValueError("ROI type {} ({}) not implemented.".format(
roi_type_value, type(roi_type_value)))
return rois, content